Project Summary

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This research addresses at least three critical needs identified in Regional Program documents. 1) the need for long-term information to assess trends in wild Chinook salmon populations; 2) the need for evaluation of broad scale population sampling and inventory methods; and 3) the need for analysis of the spatial structure of wild Chinook salmon populations.

Council Condition #1
Qualifications: The project is adequately justified for this review cycle, but to justify continuation beyond this cycle, the proponents need to establish a clearer linkage between the spatial, persistence, and genetic objectives and population viability analysis, recovery planning, and restoration implementation both in the interior Columbia River Basin planning domain and other ESA salmon recovery regions. There is not an apparent a priori viability analysis for this data to plug into. How does this inform viability analysis and restoration planning in other areas? They have high quality habitat throughout the Middle Fork Salmon River, so results could not inform poor versus good habitat, rather it informs connectivity and size of good habitat as it relates to productivity.

Qualification: The project is adequately justified for this review cycle, but to justify continuation beyond this cycle, the proponents need to establish a clearer linkage between the spatial, persistence, and genetic objectives and population viability analysis, recovery planning, and restoration implementation both in the interior Columbia River Basin planning domain and other ESA salmon recovery regions. There is not an apparent a priori viability analysis for this data to plug into. How does this inform viability analysis and restoration planning in other areas? They have high quality habitat throughout the Middle Fork Salmon River, so results could not inform poor versus good habitat, rather it informs connectivity and size of good habitat as it relates to productivity.

Summary: The project has several strong points: it has been valuable in advancing our understanding of Chinook redd placement and our ability to count redds, its research team is talented and energetic, and the fact that it has been gathering a prolonged dataset deserves special merit. But based on the current proposal the ISRP believes it might be time to think of it as being successfully completed.

The proponents “have 15 years of data, redds georeferenced at a very fine scale, and descriptions of water temperatures and other characteristics across about 800 km of spawning habitat, these data will enable us to monitor potential changes in spawning site selection by Chinook salmon that will be reflected in changes in habitat characteristics as well as redd distributions.” These data provide a “tremendous analytical potential.”

Unfortunately the proposal does not identify what that potential is. Nor are testable hypotheses put forward for this funding cycle. The statement is made that the relevance of patch size/isolation/landscape theory to Chinook is unknown, and that is viewed by some as reason to hope for new insights to come, but to the ISRP that is not convincing.

As a practical matter, it is not apparent what several additional years of data would contribute to assessing Chinook salmon persistence at the population, MPG, and ESU scales? Nothing in the proposal is compelling. The ISRP could be more supportive if valuable and relevant testable hypotheses were provided.

Since this is a long-term data set, it is valuable to maintain for the interim time period. Based on the proposal, and NOAA memo, the redd counts obtained for spring Chinook in the MFSR have contributed to establishing the status and trends from this entirely natural (sub) population of Snake River ESU spring/summer Chinook. On this basis the project (and proposal) meets criteria. The data have been used to establish expansion metrics for Idaho Department of Fish and Game redd counts from index sections in the Middle Fork Salmon River.

The importance of the present funding request hinges on how valuable the long-term data set for Chinook salmon redds in MFSR is, and whether it should be continued. The request is strictly for flying time. Despite the considerable text in the proposal, there is no research component for which funding is requested. It is essentially monitoring, with potential for significant research applications. Those proposing this work have the research qualifications to make sense of the data in broader contexts such as landscape/landscape genetics and fish movement applications. This data set appears to be of sufficient value (and long-term potential value) to the Fish and Wildlife Program to continue its implementation.

This is one of a handful of projects in the Columbia River Basin where the primary focus is on the analysis of spatial structure in a salmon population - in this case spring-summer Chinook salmon in the Middle Fork of the Salmon River (MFSR). The MFSR is a uniquely valuable study area because it lies mostly within a designated wilderness, has not been heavily altered by anthropogenic disturbance, has little hatchery influence, and is used by naturally-produced fish that spawn in multiple locations throughout the drainage system. The technical background was clearly explained, and its importance to regional programs was adequately documented. The objectives of the project are relatively modest (although the geographical scale is quite large), and the budget request is primarily for helicopter time to continue the redd surveys. The addition of a geneticist to the team has provided the opportunity to compare genetic structure among local Chinook spawning populations in the MFSR and has yielded new insights into genetic variability in a major population group that is constantly expanding and contracting. The finding that, to date, genetic diversity has persisted through periods where adult escapements have varied about 100-fold since 1995 (20-2,271 redds) seems important.

From the proposal: “Our study has two primary objectives: 1) to monitor wild Chinook salmon distribution, abundance, and trend by mapping the annual distribution of Chinook salmon redds across the entire MFSR; and 2) to assess spatial and temporal patterns in extinction and colonization dynamics of wild Chinook salmon. We have two secondary objectives: 3) to describe both individual and population level wild Chinook salmon genetic variation; and 4) to evaluate methods for measuring wild Chinook salmon dispersal and for describing salmon life history patterns.”

Objective 1. Redd counts - adequate, and apparently needed.

Objective 2. Assess spatial and temporal patterns - no budget requested. From the proposal it is not clear how the assessment and analysis is to proceed or how many years of data will be required. The question of patch size and spatial distribution of restoration sites is important to salmon management. This question comes up when attempting to consider the biological benefit from a variety of restoration strategies (riparian and stream improvement, flood plain reconnection, etc). Does placement across a landscape matter? It is not entirely evident that this project will advance the understanding of this challenge in a timely manner.

Objective 3. It is not clear how this objective will be completed. Archiving the samples is excellent. But, collaboration needs to be established to further the analysis. Some top-down direction to establish coordination between this project and NOAA or CRITFC projects might be needed.

Objective 4. This objective is worth pursuing. It would be valuable to know the within tributary straying and homing tendencies of these fish. It would seem that information would contribute to developing models of recovery potential from dispersing adults.

Apparently IDFG uses data from this project to expand index area redd counts to arrive at a total count. This needs to be explained in a bit more detail. The text makes it sound like IDFG are expanding MFSR index redd counts. But the text also makes it sound like this project is collecting the essential MFSR data.

Finally, the MFSR has undergone substantial disturbance in the last few years – forest fires followed by landslides and debris torrents in the river. Major rapids have been rearranged. Incorporating disturbance regions into the geospatial models should be considered.

2. History: Accomplishments, Results, and Adaptive Management

Although the proposal states that there have been problems with filing accomplishment reports with BPA, the project’s publication record is good and papers have appeared in high quality journals. Highlights of some of the project’s key findings were included in the proposal, making the project more understandable and its importance clear. A little more information could have been presented on habitat conditions in the MFSR. For example, has the distribution of suitable spawning substrates changed over the past 15 years as a result of wildfires, and if so what might the implications be for Chinook spawning and rearing? A definition of “patch connectivity” (Si) would have been helpful, since connectivity between suitable spawning locations is critical to understanding spatial changes in spawning distribution.

The project proponent’s responses to previous ISRP questions and suggestions were thoughtful.

It was helpful to know what other interest groups (e.g., Interior Columbia Technical Recovery Team) have used data from this project, but have any policies or management actions changed as a result of the project’s findings?

Major accomplishments:

1. Establishing and maintaining redd counts for MFSR spring Chinook is apparently important. A cross walk with the ASMS would be helpful to confirm that this effort does not duplicate other assessments of spring Chinook and that the data can be combined with IDFG (and other) assessments for VSP parameters.

2. A significant amount of effort went into analyzing alternative redd sampling designs. It is not clear to what extent that analysis is reflected in other redd sampling programs in the Columbia River Basin.

3. Collection of otolith and fin tissue is important, but some effort at developing analysis is needed.

4. Collaboration is needed to complete the genetic analysis. CRITFC has a broad scale analysis of stock structure, and NOAA has a project to evaluate Snake River ESU spring Chinook independent population/MPG boundaries. These projects should be in collaboration to genotype these fish.

5. The landscape analysis of the redd count data is interesting, and some effort needs to be committed to outlining how the data will be analyzed and incorporated into recovery planning and delisting criteria for VSP parameters life-history diversity and spatial distribution. How many years of data are needed before analysis and incorporation into management strategies?

Although this project shares data with a variety of other research organizations, it is not aimed at addressing limiting factors. Rather, it seeks to examine the spatial distribution and genetic structure of a naturally spawning population in a largely wilderness-dominated watershed. It is highly unlikely that the enormous variation in adult Chinook escapement to the MFSR over the past 15 years has resulted from changes in habitat within the MFSR system; instead, the variation has likely been driven by factors such as ocean conditions operating outside the system. That does not lessen the potential importance of the project, however. Adult returns will rise and fall according to a very large suite of factors, and this work will help us understand how changes in spawning population size affect occupancy of suitable habitats within natal streams in an essentially unmanaged drainage. This information will be helpful for interpreting changes in VSP parameters that simultaneously take place in other systems in which restoration programs are occurring.

4. Deliverables, Work Elements, Metrics, and Methods

Deliverables, work elements, metrics and methods are, in general, adequately described. It would have been helpful to present a bit more information on the aerial redd counts. How often are the streams flown? What procedures are in place to correct for bias or error (e.g., double counting a redd on separate occasions, or missing a redd), and how are confidence intervals computed for spawning survey data?

It would seem that streamflow would be an important variable in influencing the distribution of adult Chinook. Are any discharge estimates available for the MFSR streams, and can this information be used to track habitat occupancy during wet or dry years?

How are the data transmitted to Taurus? The proposal mentions WordPerfect as the word processor and QPro as the database management software, but these are not widely used programs.

Qualification: The project is adequately justified for this review cycle, but to justify continuation beyond this cycle, the proponents need to establish a clearer linkage between the spatial, persistence, and genetic objectives and population viability analysis, recovery planning, and restoration implementation both in the interior Columbia River Basin planning domain and other ESA salmon recovery regions. There is not an apparent a priori viability analysis for this data to plug into. How does this inform viability analysis and restoration planning in other areas? They have high quality habitat throughout the Middle Fork Salmon River, so results could not inform poor versus good habitat, rather it informs connectivity and size of good habitat as it relates to productivity.

Summary: The project has several strong points: it has been valuable in advancing our understanding of Chinook redd placement and our ability to count redds, its research team is talented and energetic, and the fact that it has been gathering a prolonged dataset deserves special merit. But based on the current proposal the ISRP believes it might be time to think of it as being successfully completed.

The proponents “have 15 years of data, redds georeferenced at a very fine scale, and descriptions of water temperatures and other characteristics across about 800 km of spawning habitat, these data will enable us to monitor potential changes in spawning site selection by Chinook salmon that will be reflected in changes in habitat characteristics as well as redd distributions.” These data provide a “tremendous analytical potential.”

Unfortunately the proposal does not identify what that potential is. Nor are testable hypotheses put forward for this funding cycle. The statement is made that the relevance of patch size/isolation/landscape theory to Chinook is unknown, and that is viewed by some as reason to hope for new insights to come, but to the ISRP that is not convincing.

As a practical matter, it is not apparent what several additional years of data would contribute to assessing Chinook salmon persistence at the population, MPG, and ESU scales? Nothing in the proposal is compelling. The ISRP could be more supportive if valuable and relevant testable hypotheses were provided.

Since this is a long-term data set, it is valuable to maintain for the interim time period. Based on the proposal, and NOAA memo, the redd counts obtained for spring Chinook in the MFSR have contributed to establishing the status and trends from this entirely natural (sub) population of Snake River ESU spring/summer Chinook. On this basis the project (and proposal) meets criteria. The data have been used to establish expansion metrics for Idaho Department of Fish and Game redd counts from index sections in the Middle Fork Salmon River.

The importance of the present funding request hinges on how valuable the long-term data set for Chinook salmon redds in MFSR is, and whether it should be continued. The request is strictly for flying time. Despite the considerable text in the proposal, there is no research component for which funding is requested. It is essentially monitoring, with potential for significant research applications. Those proposing this work have the research qualifications to make sense of the data in broader contexts such as landscape/landscape genetics and fish movement applications. This data set appears to be of sufficient value (and long-term potential value) to the Fish and Wildlife Program to continue its implementation.

This is one of a handful of projects in the Columbia River Basin where the primary focus is on the analysis of spatial structure in a salmon population - in this case spring-summer Chinook salmon in the Middle Fork of the Salmon River (MFSR). The MFSR is a uniquely valuable study area because it lies mostly within a designated wilderness, has not been heavily altered by anthropogenic disturbance, has little hatchery influence, and is used by naturally-produced fish that spawn in multiple locations throughout the drainage system. The technical background was clearly explained, and its importance to regional programs was adequately documented. The objectives of the project are relatively modest (although the geographical scale is quite large), and the budget request is primarily for helicopter time to continue the redd surveys. The addition of a geneticist to the team has provided the opportunity to compare genetic structure among local Chinook spawning populations in the MFSR and has yielded new insights into genetic variability in a major population group that is constantly expanding and contracting. The finding that, to date, genetic diversity has persisted through periods where adult escapements have varied about 100-fold since 1995 (20-2,271 redds) seems important.

From the proposal: “Our study has two primary objectives: 1) to monitor wild Chinook salmon distribution, abundance, and trend by mapping the annual distribution of Chinook salmon redds across the entire MFSR; and 2) to assess spatial and temporal patterns in extinction and colonization dynamics of wild Chinook salmon. We have two secondary objectives: 3) to describe both individual and population level wild Chinook salmon genetic variation; and 4) to evaluate methods for measuring wild Chinook salmon dispersal and for describing salmon life history patterns.”

Objective 1. Redd counts - adequate, and apparently needed.

Objective 2. Assess spatial and temporal patterns - no budget requested. From the proposal it is not clear how the assessment and analysis is to proceed or how many years of data will be required. The question of patch size and spatial distribution of restoration sites is important to salmon management. This question comes up when attempting to consider the biological benefit from a variety of restoration strategies (riparian and stream improvement, flood plain reconnection, etc). Does placement across a landscape matter? It is not entirely evident that this project will advance the understanding of this challenge in a timely manner.

Objective 3. It is not clear how this objective will be completed. Archiving the samples is excellent. But, collaboration needs to be established to further the analysis. Some top-down direction to establish coordination between this project and NOAA or CRITFC projects might be needed.

Objective 4. This objective is worth pursuing. It would be valuable to know the within tributary straying and homing tendencies of these fish. It would seem that information would contribute to developing models of recovery potential from dispersing adults.

Apparently IDFG uses data from this project to expand index area redd counts to arrive at a total count. This needs to be explained in a bit more detail. The text makes it sound like IDFG are expanding MFSR index redd counts. But the text also makes it sound like this project is collecting the essential MFSR data.

Finally, the MFSR has undergone substantial disturbance in the last few years – forest fires followed by landslides and debris torrents in the river. Major rapids have been rearranged. Incorporating disturbance regions into the geospatial models should be considered.

2. History: Accomplishments, Results, and Adaptive Management

Although the proposal states that there have been problems with filing accomplishment reports with BPA, the project’s publication record is good and papers have appeared in high quality journals. Highlights of some of the project’s key findings were included in the proposal, making the project more understandable and its importance clear. A little more information could have been presented on habitat conditions in the MFSR. For example, has the distribution of suitable spawning substrates changed over the past 15 years as a result of wildfires, and if so what might the implications be for Chinook spawning and rearing? A definition of “patch connectivity” (Si) would have been helpful, since connectivity between suitable spawning locations is critical to understanding spatial changes in spawning distribution.

The project proponent’s responses to previous ISRP questions and suggestions were thoughtful.

It was helpful to know what other interest groups (e.g., Interior Columbia Technical Recovery Team) have used data from this project, but have any policies or management actions changed as a result of the project’s findings?

Major accomplishments:

1. Establishing and maintaining redd counts for MFSR spring Chinook is apparently important. A cross walk with the ASMS would be helpful to confirm that this effort does not duplicate other assessments of spring Chinook and that the data can be combined with IDFG (and other) assessments for VSP parameters.

2. A significant amount of effort went into analyzing alternative redd sampling designs. It is not clear to what extent that analysis is reflected in other redd sampling programs in the Columbia River Basin.

3. Collection of otolith and fin tissue is important, but some effort at developing analysis is needed.

4. Collaboration is needed to complete the genetic analysis. CRITFC has a broad scale analysis of stock structure, and NOAA has a project to evaluate Snake River ESU spring Chinook independent population/MPG boundaries. These projects should be in collaboration to genotype these fish.

5. The landscape analysis of the redd count data is interesting, and some effort needs to be committed to outlining how the data will be analyzed and incorporated into recovery planning and delisting criteria for VSP parameters life-history diversity and spatial distribution. How many years of data are needed before analysis and incorporation into management strategies?

Although this project shares data with a variety of other research organizations, it is not aimed at addressing limiting factors. Rather, it seeks to examine the spatial distribution and genetic structure of a naturally spawning population in a largely wilderness-dominated watershed. It is highly unlikely that the enormous variation in adult Chinook escapement to the MFSR over the past 15 years has resulted from changes in habitat within the MFSR system; instead, the variation has likely been driven by factors such as ocean conditions operating outside the system. That does not lessen the potential importance of the project, however. Adult returns will rise and fall according to a very large suite of factors, and this work will help us understand how changes in spawning population size affect occupancy of suitable habitats within natal streams in an essentially unmanaged drainage. This information will be helpful for interpreting changes in VSP parameters that simultaneously take place in other systems in which restoration programs are occurring.

4. Deliverables, Work Elements, Metrics, and Methods

Deliverables, work elements, metrics and methods are, in general, adequately described. It would have been helpful to present a bit more information on the aerial redd counts. How often are the streams flown? What procedures are in place to correct for bias or error (e.g., double counting a redd on separate occasions, or missing a redd), and how are confidence intervals computed for spawning survey data?

It would seem that streamflow would be an important variable in influencing the distribution of adult Chinook. Are any discharge estimates available for the MFSR streams, and can this information be used to track habitat occupancy during wet or dry years?

How are the data transmitted to Taurus? The proposal mentions WordPerfect as the word processor and QPro as the database management software, but these are not widely used programs.

BiOp Workgroup Comments: For compliance with RPA 50.7: This RPA action is for hatchery fish marking only. Confirm that the scope of work proposed is for 100% marking of fish (visible or non visible) from the hatchery supported. If this project is marking fish for the hatchery, please specify the hatchery name and populations affected. If marking is conducted under another project or program, please let us know the name of that project/program.

The BiOp RM&E Workgroups made the following determinations regarding the proposal's ability or need to support BiOp Research, Monitoring and Evaluation (RME) RPAs. If you have questions regarding these RPA association conclusions, please contact your BPA COTR and they will help clarify, or they will arrange further discussion with the appropriate RM&E Workgroup Leads. BiOp RPA associations for the proposed work are: ( 50.6 51.1 ) All Questionable RPA Associations ( ) and All Deleted RPA Associations (50.1 50.2 50.3 50.4 50.5 50.7 50.8 51.2 51.3 56.1 56.2 56.3 64.2)

Proponent Response:

I respectfully request an opportunity to have further discussions with the appropriate RM&E workgroup leads.

Until I received the 1/20/2011 email from Brian Mercier, I was not aware that there were RPA sub-actions listed for each RPA. Consequently, when I drafted this proposal, I only listed the RPA numbers (50,51,56) that, based on their focus, were determined to be linked to the project. I was not aware that I needed to view a list of subactions and sort out the subactions (i.e., 50.1, 50.2, etc.) that do not apply and list those (i.e., 50.6) that do apply. I have never seen the subaction list and have never seen an explanation of the subactions that may apply to my project. For example, RPA 56 is titled: "Monitor and evaluate tributary habitat conditions and limiting factors" I address that question in this project so listed RPA 56 as being met. Apparently the RPA 56 subactions address very specific objectives or areas so do not apply to my project? Since I have never seen a list and explanation of the RPA subactions it was impossible for me to determine which apply.

As a result, I request that the appropriate RM&E workgroup leads please inform me how to view a complete RPA subaction list with explanations of the RPA subactions for RPAs 50,51, and 56 and any others that may apply to this project.

Finally, the comments above also listed RPA 64.2. Since I did not list RPA 64 on pg 2 of the proposal, it is unclear why that was referenced as not applying?

Thank You

I look forward to further discussions to improve my understanding of the RPA process.

The sponsors propose to continue aerial surveys of the Middle Fork Salmon River to fully census spring and summer Chinook salmon redds, collect tissue from spawning Chinook in remote areas to add to tissue collections used to produce genotypic data, and perform correlative and cross-wavelet analysis of the relationship between the location of Chinook salmon redds and landscape features. The quality of the work and publication trail is excellent.

The data on the spatial and temporal variation in Chinook salmon redds is used in recovery planning by State, Federal, and Tribal agencies. The analysis of the relationship between environmental factors and spatial and temporal variation in redd (Chinook) abundance will add to the basic understanding of the persistence of Chinook salmon metapopulations. On this basis the ISRP believes this effort is justified.

At this time, the ISRP also qualifies the support for this activity. Specifically, there is a merging of research (the analysis of relationships between habitat conditions and redd abundance, and comparisons of index versus full census of redd counts) and annual trend monitoring of adult Chinook abundance via redd counts. These two functions of this proposal need to be clearly identified, and the research component needs to be justified in the future based on its broader application to the Snake and/or Salmon River systems. The project's publication record is excellent, but there is a lack of evidence that what is being learned is being translated into either modified sampling schemes, innovative analyses of persistence by TRTs, or modified land use management in other watersheds. There is a point of diminishing returns in any research effort. The level of effort for the trend monitoring and for the research components in the future needs to reflect data needs and the incorporation of the research products into management actions.

There are still vast amounts of spatial information collected on Chinook redds (in relation to habitat factors) to analyze and publish, so it is difficult to justify collecting even more. Managers might be consulted to determine the aspects of the data they are particularly interested in.

Finally, the next generation of space imagery may provide sufficient resolution to count redds, and this might be useful as a tool in sampling and monitoring salmon populations. This technology would greatly improve the efficiency and effectiveness of sampling and monitoring salmon populations.